Coverage ribosomal RNA

Absolute (left) and relative read coverage (right) of the ribosomal 45S template. The plot show the read abundance in comparison to the alignment position on the reference.

Coverage of ribosomal templates

Relative and absolute abundance of reads associated to known ribosomal templates. The used templates have been determined by third party research projects. The association of reads to literature based templates is performed by determining the minimal overlap of each template-read pair. The template showing maximal overlap between all possible template-read pairs is determined as associated reference.

Taillenght of ribosomal templates

Interactive relative abundance plots of template associated reads. The three plots show the reference based cut sites on the 45S reference (top), the minimal and maximal of cut sites (center) and the mean start and end sites (bottom) of the associated reads. The mean taillength and standard deviation is shown for each template. The violinplot shows the taillength distributions for each template. The association of reads to literature based templates is performed by determining the minimal overlap of each template-read pair. The template showing a maximal overlap between all possible template-read pairs is determined as reference for the given read. PolyA taillength is determined with the polya tail prediction function integrated in dorado.

Cut sites

Cut sites occurring in significant abundance in relation to the gaussian distribution of cut sites of literature based templates. Relative cut site abundance has been normalized by the absolute number of reads aligning to the 45S reference. For intersecting templates the significance threshold has been determined by the combined gaussian of both fragments.

Intensity matrix

The intensity matrix plot shows the min-max normalized amount of reads sharing the same start and end points on the 45S reference after alignment (top). The interactive plot (bottom) represents a sub sampled version of the intensity matrix showing the 25000 most abundant clusters.

Intensity Clustering

Interactive plot showing the min max normalized abundance and position on 45S reference of read clusters determined by reads sharing the same start and end sites on the 45S matrix. The 300 biggest clusters are visualized. Additionally, the mean and stdd of polyA-tails of the clusters are shown. The taillength is determined by the polya tail prediction function integrated in dorado. For validation of the clustering approach the 300 biggest clusters are shown as squares above the instensity matrix ranging from start to end of reference on the coordinate system. The Upper left corner should allocate with a cluster showing a high intensity or read density.

HDBSCAN Clustering

Interactive plot showing the min max normalized abundance and position on 45S reference of read clusters determined by density based clustering approach using the intensity matrix as template. The 300 biggest clusters are visualized. Additionally, the mean and stdd of polyA-tails of the clusters are shown. The taillength is determined by the polya tail prediction function integrated in dorado. For validation of the clustering approach the 300 biggest clusters are shown as squares above the instensity matrix ranging from start to end of reference on the coordinate system. The Upper left corner should allocate with a cluster showing a high intensity or read density.

Modifications on ribosomal template

Relative modification abundance plots for pseU (top) and m6A (bottom) modifications over the 45S reference. The modification detection is performed with the integrated dorado models for modification detection. In the pseU plot the systematic C/U missmatch reported for pseU is added, since the dorado models are not taking missbasecalled bases in consideration.